ITK配准：基于手动设置配准点的图像配准

本例子是通过手动设置定标点对待配准图像进行移动，使其与参考图像配准！

本文是基于位移场将图像进行wrap操作，以实现最终的配准！该实现是基于WarpImageFilter 进行操作的，WarpImageFilter 在给定的位移场的作用下将已有图像进行wrap（空间扭曲）操作。位移场可以看做是一张图像，其pixel type是长度至少为N的向量型（vector type）。其中N是输入图像的维数。位移场中每个向量表示输入空间中的几何点和输出空间上点的距离。P(in)=P(out)+d。

WarpImageFilter的输出是通过逆向映射实现的，输出像素被映射到输入图像。该方案避免了创建输出图像中的任何漏洞和重叠。在映射过程中存在不能映射到输入图像的整数位置，所以需要用到插值函数，用以计算在非整数位置的像素值。默认的插值方式是 LinearInterpolateImageFunction，可以通过 SetInterpolator()来进行设置。
映射到输入图像缓冲区的外部的位置，将分配一个边缘填充的值。

1、生成图像

参考图为：像素尺寸100X100，在以（40,40）和（60,60）为坐标所包围的区域像素值为255，其余区域像素值为0；

待配准图为：像素尺寸100X100，在以（20,20）和（80,80）为坐标所包围的区域像素值为100，其余区域像素值为0；

在配准的过程手动设置移动场源的定标点，即为配准导航点。

2、基于两个定标集合（即所谓的导航点，也称为简单称为配准点）产生位移场（displacement field）

1）设置形变场源对象的参数时，向参考图看起，如deformationFieldSource->SetOutputSpacing( fixedImage->GetSpacing() );等

2）生成参考图和待配准图的landmarks，即两者的地标！通过InsertElement( 2, sourcePoint );对地标点进行添加！

3）将地标点与形变场源进行关联

3、建立一个WarpImageFilterType的warpImageFilter。

1）需要设置其所对应的插值器

2）根据形变场源设置warpImageFilter的SetOutputSpacing和SetOutputOrigin

3）需要将其与2中的形变场源进行关联。warpImageFilter->SetDisplacementField( deformationFieldSource->GetOutput() );

同时也需要设置其待配准图像的输入：warpImageFilter->SetInput( movingImage );

4、输出配准结果

只需要利用一个writer将warpImageFilter的结果进行输出即可！

writer->SetInput (  warpImageFilter->GetOutput() );

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImage.h"
#include "itkVector.h"
#if ITK_VERSION_MAJOR < 4
#include "itkDeformationFieldSource.h"
#else
#include "itkLandmarkDisplacementFieldSource.h"
#endif

#include "itkWarpImageFilter.h"

const     unsigned int   Dimension = 2;
typedef   unsigned char  PixelType;
typedef   itk::Image< PixelType, Dimension > ImageType;

static void CreateFixedImage(ImageType::Pointer image);
static void CreateMovingImage(ImageType::Pointer image);

int main(int, char *[])
{
	typedef   float          VectorComponentType;

	typedef   itk::Vector< VectorComponentType, Dimension >    VectorType;
	typedef   itk::Image< VectorType,  Dimension >   DeformationFieldType;

	ImageType::Pointer fixedImage =
		ImageType::New();
	CreateFixedImage(fixedImage);

	ImageType::Pointer movingImage =
		ImageType::New();
	CreateMovingImage(movingImage);
//Computes a displacement field(位移场) from two sets of landmarks. 
#if ITK_VERSION_MAJOR < 4
	typedef itk::DeformationFieldSource<DeformationFieldType>  DeformationFieldSourceType;
#else
	typedef itk::LandmarkDisplacementFieldSource<DeformationFieldType>  DeformationFieldSourceType;
#endif
	DeformationFieldSourceType::Pointer deformationFieldSource =
		DeformationFieldSourceType::New();
	//std::cout<<fixedImage->GetSpacing();
	deformationFieldSource->SetOutputSpacing( fixedImage->GetSpacing() );//以参考图作为输入
	deformationFieldSource->SetOutputOrigin(  fixedImage->GetOrigin() );
	deformationFieldSource->SetOutputRegion(  fixedImage->GetLargestPossibleRegion() );
	deformationFieldSource->SetOutputDirection( fixedImage->GetDirection() );

	//  Create source and target landmarks.
	typedef DeformationFieldSourceType::LandmarkContainerPointer   LandmarkContainerPointer;
	typedef DeformationFieldSourceType::LandmarkContainer          LandmarkContainerType;
	typedef DeformationFieldSourceType::LandmarkPointType          LandmarkPointType;

	LandmarkContainerType::Pointer sourceLandmarks =
		LandmarkContainerType::New();
	LandmarkContainerType::Pointer targetLandmarks =
		LandmarkContainerType::New();

	LandmarkPointType sourcePoint;
	LandmarkPointType targetPoint;

	//设置进行配准的起始位置
	sourcePoint[0] = 40;//参考图像遍历的起始位置，坐标表示！
	sourcePoint[1] = 40;
	targetPoint[0] = 20;//待配准图像遍历的起始位置，坐标表示！
	targetPoint[1] = 20;
	sourceLandmarks->InsertElement( 0, sourcePoint );
	targetLandmarks->InsertElement( 0, targetPoint );

	sourcePoint[0] = 40;//设置第二个配准点
	sourcePoint[1] = 60;
	targetPoint[0] = 20;
	targetPoint[1] = 80;
	sourceLandmarks->InsertElement( 1, sourcePoint );
	targetLandmarks->InsertElement( 1, targetPoint );

	sourcePoint[0] = 60;//设置第3个配准点！
	sourcePoint[1] = 40;
	targetPoint[0] = 80;
	targetPoint[1] = 20;
	sourceLandmarks->InsertElement( 2, sourcePoint );
	targetLandmarks->InsertElement( 2, targetPoint );

	sourcePoint[0] = 60;//设置第4个配准点
	sourcePoint[1] = 60;
	targetPoint[0] = 80;
	targetPoint[1] = 80;
	sourceLandmarks->InsertElement( 3, sourcePoint );
	targetLandmarks->InsertElement( 3, targetPoint );
	//设置形变场场源！将其与配准点进行关联
	deformationFieldSource->SetSourceLandmarks( sourceLandmarks.GetPointer() );
	deformationFieldSource->SetTargetLandmarks( targetLandmarks.GetPointer() );
	deformationFieldSource->UpdateLargestPossibleRegion();

	// Write the deformation field
	{
		typedef itk::ImageFileWriter<  DeformationFieldType  > WriterType;
		WriterType::Pointer writer =
			WriterType::New();
		writer->SetInput (  deformationFieldSource->GetOutput() );
		writer->SetFileName( "deformation.mhd" );
		writer->Update();
	}


	typedef itk::WarpImageFilter< ImageType,
		ImageType,
		DeformationFieldType  >  WarpImageFilterType;

	WarpImageFilterType::Pointer warpImageFilter =
		WarpImageFilterType::New();
	//插值器类型
	typedef itk::LinearInterpolateImageFunction<ImageType, double >  InterpolatorType;
	InterpolatorType::Pointer interpolator =
		InterpolatorType::New();

	warpImageFilter->SetInterpolator( interpolator );
	warpImageFilter->SetOutputSpacing( deformationFieldSource->GetOutput()->GetSpacing() );
	warpImageFilter->SetOutputOrigin(  deformationFieldSource->GetOutput()->GetOrigin() );
#if ITK_VERSION_MAJOR < 4
	warpImageFilter->SetDeformationField( deformationFieldSource->GetOutput() );
#else
	warpImageFilter->SetDisplacementField( deformationFieldSource->GetOutput() );
#endif
	warpImageFilter->SetInput( movingImage );
	warpImageFilter->Update();

	// Write the output
	typedef itk::ImageFileWriter<  ImageType  > WriterType;
	WriterType::Pointer writer =
		WriterType::New();
	writer->SetInput (  warpImageFilter->GetOutput() );
	writer->SetFileName( "output.png" );
	writer->Update();

	return EXIT_SUCCESS;
}

void CreateFixedImage(ImageType::Pointer image)
{
	// Create a black image with a white square
	//参考图像为（40,40）和（60,60）之间所包围的一个矩形框，且该区域灰度值为255
	ImageType::IndexType start;
	start.Fill(0);

	ImageType::SizeType size;
	size.Fill(100);

	ImageType::RegionType region;
	region.SetSize(size);
	region.SetIndex(start);

	image->SetRegions(region);
	image->Allocate();
	image->FillBuffer(0);

	itk::ImageRegionIterator<ImageType> imageIterator(image,region);

	while(!imageIterator.IsAtEnd())
	{
		if(imageIterator.GetIndex()[0] > 40 && imageIterator.GetIndex()[0] < 60 &&
			imageIterator.GetIndex()[1] > 40 && imageIterator.GetIndex()[1] < 60)
		{
			imageIterator.Set(255);
		}
		++imageIterator;
	}

	// Write the deformation field
	typedef itk::ImageFileWriter<  ImageType  > WriterType;
	WriterType::Pointer writer =
		WriterType::New();
	writer->SetInput (  image );
	writer->SetFileName( "fixed.png" );
	writer->Update();
}


void CreateMovingImage(ImageType::Pointer image)
{
	// Create a black image with a white square
	//待配准图像为(20,20)和（80,80）所围成的矩形框，且该区域灰度值为100
	ImageType::IndexType start;
	start.Fill(0);

	ImageType::SizeType size;
	size.Fill(100);

	ImageType::RegionType region;
	region.SetSize(size);
	region.SetIndex(start);

	image->SetRegions(region);
	image->Allocate();
	image->FillBuffer(0);

	itk::ImageRegionIterator<ImageType> imageIterator(image,region);

	while(!imageIterator.IsAtEnd())
	{
		if(imageIterator.GetIndex()[0] > 20 && imageIterator.GetIndex()[0] < 80 &&
			imageIterator.GetIndex()[1] > 20 && imageIterator.GetIndex()[1] < 80)
		{
			imageIterator.Set(100);
		}
		++imageIterator;
	}

	// Write the deformation field
	typedef itk::ImageFileWriter<  ImageType  > WriterType;
	WriterType::Pointer writer =
		WriterType::New();
	writer->SetInput (  image );
	writer->SetFileName( "moving.png" );
	writer->Update();
}

结果图如下所示：